By AdjAssocProf Clare Stirzaker

Journal articles

Korbie D; Lin E; Wall D; Nair SS; Stirzaker C; Clark SJ; Trau M, 2015, 'Multiplex bisulfite PCR resequencing of clinical FFPE DNA', Clinical Epigenetics, 7, pp. 28, http://dx.doi.org/10.1186/s13148-015-0067-3

Riebler A; Menigatti M; Song JZ; Statham AL; Stirzaker C; Mahmud N; Mein CA; Clark SJ; Robinson MD, 2014, 'BayMeth:Improved DNA methylation quantification for affinity capture sequencing data using a flexible Bayesian approach', Genome Biology, 15, pp. r35, http://dx.doi.org/10.1186/gb-2014-15-2-r35

Stirzaker C; Taberlay PC; Statham AL; Clark SJ, 2014, 'Mining cancer methylomes: Prospects and challenges', Trends in Genetics, 30, pp. 75 - 84, http://dx.doi.org/10.1016/j.tig.2013.11.004

Clark AK; Taubenberger AV; Taylor RA; Niranjan B; Chea ZY; Zotenko E; Sieh S; Pedersen JS; Norden S; Frydenberg M; Grummet JP; Pook DW; Stirzaker C; Clark SJ; Lawrence MG; Ellem SJ; Hutmacher DW; Risbridger GP, 2013, 'A bioengineered microenvironment to quantitatively measure the tumorigenic properties of cancer-associated fibroblasts in human prostate cancer', Biomaterials, 34, pp. 4777 - 4785, http://dx.doi.org/10.1016/j.biomaterials.2013.03.005

Hulf T; Sibbritt T; Wiklund ED; Patterson K; Song JZ; Stirzaker C; Qu W; Nair S; Horvath LG; Armstrong NJ; Kench JG; Sutherland RL; Clark SJ, 2013, 'Epigenetic-induced repression of microRNA-205 is associated with MED1 activation and a poorer prognosis in localized prostate cancer.', Oncogene, 32, pp. 2891 - 2899, http://dx.doi.org/10.1038/onc.2012.300

Bert SA; Robinson MD; Strbenac D; Statham AL; Song JZ; Hulf T; Sutherland RL; Coolen MW; Stirzaker C; Clark SJ, 2013, 'Regional Activation of the Cancer Genome by Long-Range Epigenetic Remodeling', Cancer Cell, 23, pp. 9 - 22, http://dx.doi.org/10.1016/j.ccr.2012.11.006

Valdés-Mora F; Song JZ; Statham AL; Strbenac D; Robinson MD; Nair SS; Patterson KI; Tremethick DJ; Stirzaker C; Clark SJ, 2012, 'Acetylation of H2A.Z is a key epigenetic modification associated with gene deregulation and epigenetic remodeling in cancer.', Genome Res, 22, pp. 307 - 321, http://dx.doi.org/10.1101/gr.118919.110

Statham AL; Robinson MD; Song JZ; Coolen MW; Stirzaker C; Clark SJ, 2012, 'Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA.', Genome Res, 22, pp. 1120 - 1127, http://dx.doi.org/10.1101/gr.132076.111

Robinson MD; Strbenac D; Stirzaker C; Statham AL; Song J; Speed TP; Clark SJ, 2012, 'Copy-number-aware differential analysis of quantitative DNA sequencing data.', Genome Res, 22, pp. 2489 - 2496, http://dx.doi.org/10.1101/gr.139055.112

Patterson K; Molloy L; Qu W; Clark S, 2011, 'DNA methylation: bisulphite modification and analysis.', J Vis Exp, http://dx.doi.org/10.3791/3170

Kohonen-Corish MRJ; Selinger CI; Cooper WA; Al-Sohaily S; Mladenova DN; Pangon L; Kennedy CW; McCaughan BC; Stirzaker C, 2011, 'LOSS OF SATB 1 EXPRESSION IS A MARKER OF POOR SURVIVAL IN LUNG CANCER', JOURNAL OF THORACIC ONCOLOGY, 6, pp. S4 - S4, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000287990600013&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Robinson MD; Stirzaker C; Statham AL; Coolen MW; Song JZ; Nair SS; Strbenac D; Speed TP; Clark SJ, 2011, 'Evaluation of affinity-based genome-wide DNA methylation data: Effects of CpG density, amplification bias, and copy number variation (Genome Research (2010), 20 (1719-1729))', Genome Research, 21, pp. 146

Nair SS; Coolen MW; Stirzaker C; Song JZ; Statham AL; Strbenac D; Robinson MD; Clark SJ, 2011, 'Comparison of methyl-DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain (MBD) protein capture for genome-wide DNA methylation analysis reveal CpG sequence coverage bias.', Epigenetics, 6, pp. 34 - 44, http://dx.doi.org/10.4161/epi.6.1.13313

Devaney J; Stirzaker C; Qu W; Song JZ; Statham AL; Patterson KI; Horvath LG; Tabor B; Coolen MW; Hulf T; Kench JG; Henshall SM; Pe Benito R; Haynes A-M; Mayor R; Peinado MA; Sutherland RL; Clark SJ, 2011, 'Epigenetic deregulation across chromosome 2q14.2 differentiates normal from prostate cancer and provides a regional panel of novel DNA methylation cancer biomarkers.', Cancer Epidemiol Biomarkers Prev, 20, pp. 148 - 159, http://dx.doi.org/10.1158/1055-9965.EPI-10-0719

Selinger CI; Cooper WA; Al-Sohaily S; Mladenova DN; Pangon L; Kennedy CW; McCaughan BC; Stirzaker C; Kohonen-Corish MRJ, 2011, 'Loss of special AT-rich binding protein 1 expression is a marker of poor survival in lung cancer.', J Thorac Oncol, 6, pp. 1179 - 1189, http://dx.doi.org/10.1097/JTO.0b013e31821b4ce0

Statham AL; Strbenac D; Coolen MW; Stirzaker C; Clark SJ; Robinson MD, 2010, 'Repitools: an R package for the analysis of enrichment-based epigenomic data.', Bioinformatics, 26, pp. 1662 - 1663, http://dx.doi.org/10.1093/bioinformatics/btq247

Coolen MW; Stirzaker C; Song JZ; Statham AL; Kassir Z; Moreno CS; Young AN; Varma V; Speed TP; Cowley M; Lacaze P; Kaplan W; Robinson MD; Clark SJ, 2010, 'Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity.', Nat Cell Biol, 12, pp. 235 - 246, http://dx.doi.org/10.1038/ncb2023

Robinson MD; Stirzaker C; Statham AL; Coolen MW; Song JZ; Nair SS; Strbenac D; Speed TP; Clark SJ, 2010, 'Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation.', Genome Res, 20, pp. 1719 - 1729, http://dx.doi.org/10.1101/gr.110601.110

Hinshelwood RA; Melki JR; Huschtscha LI; Paul C; Song JZ; Stirzaker C; Reddel RR; Clark SJ, 2009, 'Aberrant de novo methylation of the p16INK4A CpG island is initiated post gene silencing in association with chromatin remodelling and mimics nucleosome positioning.', Hum Mol Genet, 18, pp. 3098 - 3109, http://dx.doi.org/10.1093/hmg/ddp251

Hinshelwood RA; Huschtscha LI; Melki J; Stirzaker C; Abdipranoto A; Vissel B; Ravasi T; Wells CA; Hume DA; Reddel RR; Clark SJ, 2007, 'Concordant epigenetic silencing of transforming growth factor-beta signaling pathway genes occurs early in breast carcinogenesis.', Cancer Res, 67, pp. 11517 - 11527, http://dx.doi.org/10.1158/0008-5472.CAN-07-1284

Hitchins MP; Lin VA; Buckle A; Cheong K; Halani N; Ku S; Kwok C-T; Packham D; Suter CM; Meagher A; Stirzaker C; Clark S; Hawkins NJ; Ward RL, 2007, 'Epigenetic inactivation of a cluster of genes flanking MLH1 in microsatellite-unstable colorectal cancer.', Cancer Res, 67, pp. 9107 - 9116, http://dx.doi.org/10.1158/0008-5472.CAN-07-0869

Stirzaker C; Dia H, 2007, 'Evaluation of transportation infrastructure management strategies using microscopic traffic simulation', Journal of Infrastructure Systems, 13, pp. 168 - 174, http://dx.doi.org/10.1061/(ASCE)1076-0342(2007)13:2(168)

Clark SJ; Statham A; Stirzaker C; Molloy PL; Frommer M, 2006, 'DNA methylation: Bisulphite modification and analysis', Nature Protocols, 1, pp. 2353 - 2364, http://dx.doi.org/10.1038/nprot.2006.324

Frigola J; Song J; Stirzaker C; Hinshelwood RA; Peinado MA; Clark SJ, 2006, 'Epigenetic remodeling in colorectal cancer results in coordinate gene suppression across an entire chromosome band.', Nat Genet, 38, pp. 540 - 549, http://dx.doi.org/10.1038/ng1781

Stirzaker C; Song JZ; Davidson B; Clark SJ, 2004, 'Transcriptional gene silencing promotes DNA hypermethylation through a sequential change in chromatin modifications in cancer cells.', Cancer Res, 64, pp. 3871 - 3877, http://dx.doi.org/10.1158/0008-5472.CAN-03-3690

Song JZ; Stirzaker C; Harrison J; Melki JR; Clark SJ, 2002, 'Hypermethylation trigger of the glutathione-S-transferase gene (GSTP1) in prostate cancer cells.', Oncogene, 21, pp. 1048 - 1061, http://dx.doi.org/10.1038/sj.onc.1205153

Warnecke PM; Stirzaker C; Song J; Grunau C; Melki JR; Clark SJ, 2002, 'Identification and resolution of artifacts in bisulfite sequencing.', Methods, 27, pp. 101 - 107, http://dx.doi.org/10.1016/s1046-2023(02)00060-9

Harrison J; Stirzaker C; Clark SJ, 1998, 'Cytosines adjacent to methylated CpG sites can be partially resistant to conversion in genomic bisulfite sequencing leading to methylation artifacts.', Anal Biochem, 264, pp. 129 - 132, http://dx.doi.org/10.1006/abio.1998.2833

Warnecke PM; Stirzaker C; Melki JR; Millar DS; Paul CL; Clark SJ, 1997, 'Detection and measurement of PCR bias in quantitative methylation analysis of bisulphite-treated DNA.', Nucleic Acids Res, 25, pp. 4422 - 4426, http://dx.doi.org/10.1093/nar/25.21.4422

Stirzaker C; Millar DS; Paul CL; Warnecke PM; Harrison J; Vincent PC; Frommer M; Clark SJ, 1997, 'Extensive DNA methylation spanning the Rb promoter in retinoblastoma tumors', Cancer Research, 57, pp. 2229 - 2237

Stirzaker SC; Poncet D; Both GW, 1990, 'Sequences in rotavirus glycoprotein VP7 that mediate delayed translocation and retention of the protein in the endoplasmic reticulum', Journal of Cell Biology, 111, pp. 1343 - 1350, http://dx.doi.org/10.1083/jcb.111.4.1343

Stirzaker SC; Both GW, 1989, 'The signal peptide of the rotavirus glycoprotein VP7 is essential for its retention in the ER as an integral membrane protein', Cell, 56, pp. 741 - 747, http://dx.doi.org/10.1016/0092-8674(89)90677-6

Whitfeld PL; Tyndall C; Stirzaker SC; Bellamy AR; Both GW, 1987, 'Location of sequences within rotavirus SA11 glycoprotein VP7 which direct it to the endoplasmic reticulum.', Molecular and Cellular Biology, 7, pp. 2491 - 2497, http://dx.doi.org/10.1128/MCB.7.7.2491

Stirzaker SC; Whitfield PL; Christie DL; Bellamy AR; Both GW, 1987, 'Processing of rotavirus glycoprotein VP7: Implications for the retention of the protein in the endoplasmic reticulum', Journal of Cell Biology, 105, pp. 2897 - 2903, http://dx.doi.org/10.1083/jcb.105.6.2897

Conference Papers

Cole AJ; Dickson K-A; Liddle C; Stirzaker C; Clifton-Bligh R; Marsh DJ, 2018, 'Abstract A06: Cisplatin-induced DNA damage modifies the chromatin landscape of histone H2B monoubiquitination in a p53-dependent manner', in Clinical Cancer Research, American Association for Cancer Research (AACR), pp. A06 - A06, http://dx.doi.org/10.1158/1557-3265.ovca17-a06

Lawrence MG; Pidsley R; Zotenko E; Niranjan B; Statham A; Song J; Armstrong N; Pedersen J; Frydenberg M; Taylor R; Stirzaker C; Risbridger G; Clark S, 2017, 'Abstract 1997: Charting the DNA methylation landscape of prostate cancer associated fibroblasts', in Cancer Research, American Association for Cancer Research (AACR), pp. 1997 - 1997, http://dx.doi.org/10.1158/1538-7445.am2017-1997

Stirzaker C; Song JZ; Statham AL; Robinson M; Lacaze P; Coolen M; Moreno CS; Warren K; Clark SJ, 2009, 'CONSOLIDATION OF THE CANCER EPIGENOME TO REGIONS OF UNIFORM CHROMATIN', in CELLULAR ONCOLOGY, IOS PRESS, SCOTLAND, Edinburgh, pp. 136 - 136, presented at 3rd Marie Curie-Genome Architecture in Relation to Disease Meeting (MC-GARD), SCOTLAND, Edinburgh, 01 April 2009 - 05 April 2009, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000265635300098&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Stirzaker C; Song JZ; Statham AL; Robinson M; Lacaze P; Coolen M; Moreno CS; Warren K; Clark SJ, 2009, 'CONSOLIDATION OF THE CANCER EPIGENOME TO REGIONS OF UNIFORM CHROMATIN', in CELLULAR ONCOLOGY, SPRINGER, SCOTLAND, Edinburgh, pp. 101 - 101, presented at 3rd Marie Curie-Genome Architecture in Relation to Disease Meeting (MC-GARD), SCOTLAND, Edinburgh, 01 April 2009 - 05 April 2009, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000265635300028&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Coolen M; Song J; Statham AL; Lacaze P; Moreno CS; Kaplan W; Stirzaker C; Clark SJ, 2008, 'Long range epigenetic silencing (LRES): A common phenomenon in prostate cancer', in CELLULAR ONCOLOGY, IOS PRESS, SPAIN, Madrid, pp. 225 - 225, presented at 2nd Marie Curie-Genome Architecture in Relation to Disease Meeting (MC-GARD), SPAIN, Madrid, 04 May 2008 - 07 May 2008, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000255341800005&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Frigola J; Song JZ; Stirzaker C; Peinado MA; Clark SJ, 2006, 'Epigenetic Silent Neighborhoods in Cancer Cells', in CANCER RESEARCH, AMER ASSOC CANCER RESEARCH, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000454606204232&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Conference Abstracts

Meyer B; Stirzaker C; Ramkomuth S; Harvey K; Swarbrick A; Clark SJ; O'Toole S; Pidsley R, 2024, 'Detailed DNA methylation characterisation of phyllodes tumours identifies a signature of malignancy and distinguishes phyllodes from metaplastic breast carcinoma', in Pathology, Elsevier, Vol. 56, pp. s70 - s71, http://dx.doi.org/10.1016/j.pathol.2023.12.241

Stirzaker C; Chia KM; Portman N; Milioli HH; Clifton S; Achinger-Kawecka J; Nair S; Lim E; Clark S, 2019, 'DNA demethylation agents as a therapeutic approach in endocrine-resistant breast cancer', in Oncolabs, presented at 7th PacRim Breast & Prostate Cancer Meeting, http://dx.doi.org/10.1530/oncolabs.1.P049

Mathe A; Wong-Brown M; Morten BC; Braye SG; Locke WJ; Stirzaker C; Clark SJ; Scott R; Avery-Kiejda KA, 2018, 'Defining the Key Mediators of Breast Cancer Progression and Treatment Resistance in the triple Negative Subtype', in ASIA-PACIFIC JOURNAL OF CLINICAL ONCOLOGY, WILEY, Vol. 14, pp. 9 - 9, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000446654600003&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Blazevski A; Pidsley R; Qu W; Korbie D; Luu L; Chang J; Yuen B; Scheltema MJ; Masand N; Haynes A-M; Quoc N; Stirzaker C; Song J; Stricker P; Clark S, 2018, 'When Focal Therapy Fails for Localised Prostate Cancer - Can Epigenetics Predict Which Patients Fail and Improve Patient Selection?', in ASIA-PACIFIC JOURNAL OF CLINICAL ONCOLOGY, WILEY, Vol. 14, pp. 33 - 33, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000437670700023&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Cole AJ; Dickson K-A; Liddle C; Stirzaker C; Clifton-Bligh R; Marsh DJ, 2017, 'Cisplatin-induced DNA damage modifies the chromatin landscape of histone H2B monoubiquitination in a p53-dependent manner.', in CLINICAL CANCER RESEARCH, AMER ASSOC CANCER RESEARCH, PA, Pittsburgh, Vol. 24, pp. 40 - 41, presented at AACR Special Conference on Addressing Critical Questions in Ovarian Cancer Research and Treatment, PA, Pittsburgh, 01 October 2017 - 04 October 2017, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000440823600042&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Mathe A; Wong-Brown M; Locke W; Stirzaker C; Braye S; Forbes J; Clark S; Avery-Kiejda K; Scott R, 2016, 'DNA METHYLATION PROFILE OF TRIPLE NEGATIVE BREAST CANCER-SPECIFIC GENES COMPARING LYMPH NODE POSITIVE PATIENTS TO LYMPH NODE NEGATIVE PATIENTS', in ASIA-PACIFIC JOURNAL OF CLINICAL ONCOLOGY, WILEY-BLACKWELL, Vol. 12, pp. 27 - 27, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000387772400056&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Working Papers

Du Q; Smith GC; Luu PL; Ferguson JM; Armstrong NJ; Caldon CE; Campbell E; Nair SS; Zotenko E; Gould CM; Buckley M; Kaczorowski D; Barton K; Deveson IW; Smith MA; Powell JE; Skvortsova K; Stirzaker C; Achinger-Kawecka J; Clark SJ, DNA methylation is required to maintain DNA replication timing precision and 3D genome integrity, Cold Spring Harbor Laboratory, http://dx.doi.org10.1101/2020.10.15.338855

Preprints

So J; Chadwick TB; Fuentes-Guirado M; Vojtech L; Chi LH; Meyer B; Pidsley R; Haynes N; Chalmers H; Tabatabaee A; Ismail A; Cowley KJ; Simpson KJ; Stirzaker C; Parker BS, 2026, Targeting DNA Methylation Reactivates Type I Interferon Signalling in Bone-Metastatic Breast Cancer, http://dx.doi.org/10.64898/2026.06.28.735052

Du Q; Bert S; Armstrong N; Caldon E; Song J; Nair S; Gould C; Luu PL; Khoury A; Qu W; Zotenko E; Stirzaker C; Clark S, 2018, Replication timing shapes the cancer epigenome and the nature of chromosomal rearrangements, http://dx.doi.org/10.1101/251280

Riebler A; Menigatti M; Song JZ; Statham AL; Stirzaker C; Mahmud N; Mein CA; Clark SJ; Robinson MD, 2013, BayMeth: Improved DNA methylation quantification for affinity capture sequencing data using a flexible Bayesian approach, http://dx.doi.org/10.48550/arxiv.1312.3115

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